Dataset Information

Genotyping of human neutrophil antigens (HNA) from whole genome sequencing data.

ABSTRACT: BACKGROUND: Neutrophil antigens are involved in a variety of clinical conditions including transfusion-related acute lung injury (TRALI) and other transfusion-related diseases. Recently, there are five characterized groups of human neutrophil antigen (HNA) systems, the HNA1 to 5. Characterization of all neutrophil antigens from whole genome sequencing (WGS) data may be accomplished for revealing complete genotyping formats of neutrophil antigens collectively at genome level with molecular variations which may respectively be revealed with available genotyping techniques for neutrophil antigens conventionally. RESULTS: We developed a computing method for the genotyping of human neutrophil antigens. Six samples from two families, available from the 1000 Genomes projects, were used for a HNA typing test. There are 500 ~ 3000 reads per sample filtered from the adopted human WGS datasets in order for identifying single nucleotide polymorphisms (SNPs) of neutrophil antigens. The visualization of read alignment shows that the yield reads from WGS dataset are enough to cover all of the SNP loci for the antigen system: HNA1, HNA3, HNA4 and HNA5. Consequently, our implemented Bioinformatics tool successfully revealed HNA types on all of the six samples including sequence-based typing (SBT) as well as PCR sequence-specific oligonucleotide probes (SSOP), PCR sequence-specific primers (SSP) and PCR restriction fragment length polymorphism (RFLP) along with parentage possibility. CONCLUSIONS: The next-generation sequencing technology strives to deliver affordable and non-biased sequencing results, hence the complete genotyping formats of HNA may be reported collectively from mining the output data of WGS. The study shows the feasibility of HNA genotyping through new WGS technologies. Our proposed algorithmic methodology is implemented in a HNATyping software package with user's guide available to the public at http://sourceforge.net/projects/hnatyping/.

SUBMITTER: Chu HT

PROVIDER: S-EPMC3849977 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature

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Publications

Genotyping of human neutrophil antigens (HNA) from whole genome sequencing data.

Chu Hsueh-Ting HT Lin Han H Tsao Theresa Tsun-Hui TT Chang Chun-Fan CF Hsiao William Wl WW Yeh Tze-Jung TJ Chang Ching-Mao CM Liu Yen-Wenn YW Wang Tse-Yi TY Yang Ko-Chun KC Chen Tsung-Jui TJ Chen Jen-Chih JC Chen Kuang-Chi KC Kao Cheng-Yan CY

BMC medical genomics 20130912

<h4>Background</h4>Neutrophil antigens are involved in a variety of clinical conditions including transfusion-related acute lung injury (TRALI) and other transfusion-related diseases. Recently, there are five characterized groups of human neutrophil antigen (HNA) systems, the HNA1 to 5. Characterization of all neutrophil antigens from whole genome sequencing (WGS) data may be accomplished for revealing complete genotyping formats of neutrophil antigens collectively at genome level with molecular ...[more]

PMID: 24028078

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Project description:Genotyping-by-sequencing (GBS) represents a highly cost-effective high-throughput genotyping approach. By nature, however, GBS is subject to generating sizeable amounts of missing data and these will need to be imputed for many downstream analyses. The extent to which such missing data can be tolerated in calling SNPs has not been explored widely. In this work, we first explore the use of imputation to fill in missing genotypes in GBS datasets. Importantly, we use whole genome resequencing data to assess the accuracy of the imputed data. Using a panel of 301 soybean accessions, we show that over 62,000 SNPs could be called when tolerating up to 80% missing data, a five-fold increase over the number called when tolerating up to 20% missing data. At all levels of missing data examined (between 20% and 80%), the resulting SNP datasets were of uniformly high accuracy (96-98%). We then used imputation to combine complementary SNP datasets derived from GBS and a SNP array (SoySNP50K). We thus produced an enhanced dataset of >100,000 SNPs and the genotypes at the previously untyped loci were again imputed with a high level of accuracy (95%). Of the >4,000,000 SNPs identified through resequencing 23 accessions (among the 301 used in the GBS analysis), 1.4 million tag SNPs were used as a reference to impute this large set of SNPs on the entire panel of 301 accessions. These previously untyped loci could be imputed with around 90% accuracy. Finally, we used the 100K SNP dataset (GBS + SoySNP50K) to perform a GWAS on seed oil content within this collection of soybean accessions. Both the number of significant marker-trait associations and the peak significance levels were improved considerably using this enhanced catalog of SNPs relative to a smaller catalog resulting from GBS alone at ?20% missing data. Our results demonstrate that imputation can be used to fill in both missing genotypes and untyped loci with very high accuracy and that this leads to more powerful genetic analyses.

Project description:BackgroundAntibodies to human neutrophil alloantigens (HNA) are involved in the pathophysiology of several clinical conditions including transfusion-related acute lung injury (TRALI), alloimmune and autoimmune neutropenia, and febrile nonhemolytic transfusion reactions leading to neutropenia. The cognate antigens are polymorphic structures expressed on several glycoproteins on the neutrophils, i.e., antigens HNA-1a, -1b, -1c, and -1d on Fc-γ-receptor IIIb; HNA-2 on CD177; HNA-3a and -3b on choline transporter-like protein 2; HNA-4a and -4b on CD11b/αM subunit of the αMβ2-integrin (CD11b/CD18, Mac-1, CR3); and HNA-5a and -5b on αL-subunit (CD11a) of the αLβ2 integrin (CD11a/CD18), leukocyte function associated molecule (LFA)-1. Currently, there is a lacuna of diagnostic methods for detection of HNA in India. This study aimed to determine the HNA frequencies in Indians, estimate the risk of alloimmunization, and prepare typed neutrophil panels, which can be used to detect HNA antibodies in neutropenia cases.Material and methodsEDTA blood samples were collected from random 1,054 blood donors. HNA-2 was phenotyped on fresh EDTA samples using FITC labelled monoclonal anti-CD177 by flowcytometry. HNA-1 (FCGR3B) genotyping was carried out by DNA sequencing and PCR-RFLP. Antigens of HNA-3 (SLC44A2) and HNA-5 (ITGAL) were genotyped by PCR-RFLP using TaqαI and Bsp1286I restriction enzymes, respectively, while HNA-4 (ITGAM) was genotyped by PCR-SSP.ResultsAllele frequencies of FCGR3B*01, FCGR3B*02, and FCGR3B*03 were found to be 0.433, 0.444, and 0.087, respectively. FCGR3B*01+*02+*03- was the most common genotype (33.78%). Ten individuals showed deficiency of FCGR3B individuals, while 23 showed hyperexpression, i.e., FCGR3B*01+*02+*03+. FCGR3B*04and *05 occurred with a frequency of 0.002 and 0.024. HNA-2 was found to be a high frequency antigen occurring in 98.8% population. Four percent individuals showed atypical expression of CD177 on their neutrophils. Allele frequencies of SLC44A2*01 and SLC44A2*02were 0.812 and 0.188, respectively, and that of ITGAM*01, ITGAM*02, ITGAL*01, and ITGAL*02 were 0.9546, 0.0454, 0.2372, and 0.7628, respectively.ConclusionThis is the first study in India to report the frequencies of HNA among blood donors. Typed neutrophil panels identified in the present study will enable us to investigate suspected cases of immune neutropenia in future.

Dataset Information

Genotyping of human neutrophil antigens (HNA) from whole genome sequencing data.

Publications

Genotyping of human neutrophil antigens (HNA) from whole genome sequencing data.

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